diff --git a/pkgs/applications/terminal-emulators/terminator/default.nix b/pkgs/applications/terminal-emulators/terminator/default.nix
index aedbb761a8ca..01047f26bc63 100644
--- a/pkgs/applications/terminal-emulators/terminator/default.nix
+++ b/pkgs/applications/terminal-emulators/terminator/default.nix
@@ -30,7 +30,6 @@ python3.pkgs.buildPythonApplication rec {
     gobject-introspection
     makeBinaryWrapper
     wrapGAppsHook3
-    python3.pkgs.pytest-runner
   ];
 
   buildInputs = [
diff --git a/pkgs/development/compilers/vyper/default.nix b/pkgs/development/compilers/vyper/default.nix
index 56899b6acba4..89973eb524ee 100644
--- a/pkgs/development/compilers/vyper/default.nix
+++ b/pkgs/development/compilers/vyper/default.nix
@@ -7,7 +7,6 @@
 , importlib-metadata
 , packaging
 , pycryptodome
-, pytest-runner
 , pythonOlder
 , recommonmark
 , setuptools-scm
@@ -41,7 +40,8 @@ buildPythonPackage rec {
   postPatch = ''
     # pythonRelaxDeps doesn't work
     substituteInPlace setup.py \
-      --replace "setuptools_scm>=7.1.0,<8.0.0" "setuptools_scm>=7.1.0"
+      --replace-fail "setuptools_scm>=7.1.0,<8.0.0" "setuptools_scm>=7.1.0" \
+      --replace-fail '"pytest-runner",' ""
   '';
 
   nativeBuildInputs = [
@@ -49,7 +49,6 @@ buildPythonPackage rec {
     # ever since https://github.com/vyperlang/vyper/pull/2816
     git
 
-    pytest-runner
     setuptools-scm
   ];
 
diff --git a/pkgs/development/python-modules/hikari/default.nix b/pkgs/development/python-modules/hikari/default.nix
index 026176e7a7b8..dbc853b926aa 100644
--- a/pkgs/development/python-modules/hikari/default.nix
+++ b/pkgs/development/python-modules/hikari/default.nix
@@ -4,13 +4,12 @@
   fetchFromGitHub,
   pytestCheckHook,
   pythonOlder,
-  pytest-runner,
   aiohttp,
   attrs,
   multidict,
   colorlog,
   pynacl,
-  pytest-cov,
+  pytest-cov-stub,
   pytest-randomly,
   pytest-asyncio,
   mock,
@@ -52,9 +51,8 @@ buildPythonPackage rec {
 
   nativeCheckInputs = [
     pytestCheckHook
-    pytest-runner
     pytest-asyncio
-    pytest-cov
+    pytest-cov-stub
     pytest-randomly
     mock
   ];
diff --git a/pkgs/development/python-modules/pytest-harvest/default.nix b/pkgs/development/python-modules/pytest-harvest/default.nix
index 65325851b770..35e5945c1a62 100644
--- a/pkgs/development/python-modules/pytest-harvest/default.nix
+++ b/pkgs/development/python-modules/pytest-harvest/default.nix
@@ -3,7 +3,6 @@
   buildPythonPackage,
   fetchFromGitHub,
   setuptools-scm,
-  pytest-runner,
   pytest,
   decopatch,
   makefun,
@@ -34,11 +33,14 @@ buildPythonPackage rec {
   # we disable this file creation as it touches internet
   postPatch = ''
     echo "version = '${version}'" > pytest_harvest/_version.py
+
+    substituteInPlace pytest_harvest/tests/test_lazy_and_harvest.py \
+      --replace-fail "from distutils.version import LooseVersion" "from packaging.version import parse" \
+      --replace-fail "LooseVersion" "parse"
   '';
 
   nativeBuildInputs = [
     setuptools-scm
-    pytest-runner
   ];
 
   buildInputs = [ pytest ];
diff --git a/pkgs/development/python-modules/pytest-runner/default.nix b/pkgs/development/python-modules/pytest-runner/default.nix
deleted file mode 100644
index 57b970fc98df..000000000000
--- a/pkgs/development/python-modules/pytest-runner/default.nix
+++ /dev/null
@@ -1,40 +0,0 @@
-{
-  lib,
-  buildPythonPackage,
-  fetchPypi,
-  setuptools-scm,
-  pytest,
-}:
-
-buildPythonPackage rec {
-  pname = "pytest-runner";
-  version = "6.0.1";
-  format = "pyproject";
-
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-cNRzlYWnAI83v0kzwBP9sye4h4paafy7MxbIiILw9Js=";
-  };
-
-  postPatch = ''
-    rm pytest.ini
-  '';
-
-  nativeBuildInputs = [
-    setuptools-scm
-    pytest
-  ];
-
-  checkPhase = ''
-    py.test tests
-  '';
-
-  # Fixture not found
-  doCheck = false;
-
-  meta = with lib; {
-    description = "Invoke py.test as distutils command with dependency resolution";
-    homepage = "https://github.com/pytest-dev/pytest-runner";
-    license = licenses.mit;
-  };
-}
diff --git a/pkgs/development/python-modules/tf2onnx/default.nix b/pkgs/development/python-modules/tf2onnx/default.nix
index 73c19842f103..54a837089bc8 100644
--- a/pkgs/development/python-modules/tf2onnx/default.nix
+++ b/pkgs/development/python-modules/tf2onnx/default.nix
@@ -2,7 +2,6 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  pytest-runner,
   # runtime dependencies
   numpy,
   onnx,
@@ -34,9 +33,10 @@ buildPythonPackage rec {
     hash = "sha256-qtRzckw/KHWm3gjFwF+cPuBhGbfktjhYIwImwHn2CFk=";
   };
 
-  nativeBuildInputs = [
-    pytest-runner
-  ];
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace-fail "'pytest-runner'" ""
+  '';
 
   pythonRelaxDeps = [ "flatbuffers" ];
 
diff --git a/pkgs/development/tools/analysis/cpplint/default.nix b/pkgs/development/tools/analysis/cpplint/default.nix
index d9603ca0548d..b32e1cf4e678 100644
--- a/pkgs/development/tools/analysis/cpplint/default.nix
+++ b/pkgs/development/tools/analysis/cpplint/default.nix
@@ -35,7 +35,6 @@ python3Packages.buildPythonApplication rec {
 
   nativeCheckInputs = with python3Packages; [
     pytest
-    pytest-runner
   ];
 
   checkPhase = ''
diff --git a/pkgs/tools/backup/duplicity/default.nix b/pkgs/tools/backup/duplicity/default.nix
index 71d63a622d4d..da32f2323343 100644
--- a/pkgs/tools/backup/duplicity/default.nix
+++ b/pkgs/tools/backup/duplicity/default.nix
@@ -99,8 +99,7 @@ let self = python3.pkgs.buildPythonApplication rec {
     lockfile
     mock
     pexpect
-    pytest
-    pytest-runner
+    pytestCheckHook
     fasteners
   ]);
 
diff --git a/pkgs/tools/virtualization/udocker/default.nix b/pkgs/tools/virtualization/udocker/default.nix
index 8f0afedfd9cb..25ae2fe9ee33 100644
--- a/pkgs/tools/virtualization/udocker/default.nix
+++ b/pkgs/tools/virtualization/udocker/default.nix
@@ -17,6 +17,11 @@ python3Packages.buildPythonApplication rec {
     hash = "sha256-P49fkLvdCm/Eco+nD3SGM04PRQatBzq9CHlayueQetk=";
   };
 
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace-fail "'pytest-runner'," ""
+  '';
+
   # crun patchelf proot runc fakechroot
   # are download statistically linked during runtime
   buildInputs = [
@@ -28,7 +33,6 @@ python3Packages.buildPythonApplication rec {
   ];
 
   nativeCheckInputs = with python3Packages; [
-    pytest-runner
     pytestCheckHook
   ];
 
diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix
index f789cd32996b..3bcb357458f8 100644
--- a/pkgs/top-level/python-aliases.nix
+++ b/pkgs/top-level/python-aliases.nix
@@ -483,6 +483,7 @@ mapAliases ({
   pytest-pep8 = pytestpep8; # added 2021-01-04
   pytest-pep257 = throw "pytest-pep257 was removed, as the pep257 package was migrated into pycodestyle"; # added 2022-04-12
   pytest-pythonpath = throw "pytest-pythonpath is obsolete as of pytest 7.0.0 and has been removed"; # added 2022-03-09
+  pytest-runner = throw "pytest-runner has been removed as it uses deprecated features of setuptools and is deprecated by upstream"; # added 2024-09-15
   pytest-sanic = throw "pytest-sanic has been removed because it is unmaintained and broken"; # added 2023-06-22
   pytestpep8 = throw "pytestpep8 was removed because it is abandoned and no longer compatible with pytest v6.0"; # added 2020-12-10
   pytestquickcheck = pytest-quickcheck; # added 2021-07-20
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 5d2ecf9b584f..1014eaf703ac 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -12474,8 +12474,6 @@ self: super: with self; {
 
   pytest-responses = callPackage ../development/python-modules/pytest-responses { };
 
-  pytest-runner = callPackage ../development/python-modules/pytest-runner { };
-
   pytest-server-fixtures = callPackage ../development/python-modules/pytest-server-fixtures { };
 
   pytest-services = callPackage ../development/python-modules/pytest-services { };